[gmx-users] Error using grompp - atomtype not found

[Justin Lemkul]

On 5/26/15 3:36 AM, Sotirios Dionysios I. Papadatos wrote:
> OK, thanks but now I have a question what is the utility of a molecule.itp. You could just add the parameters from the beginning in ffbonded, nonbonded, atomtypes etc. Now it feels like I have to do double the work.

There are two approaches.

1. Define new parameters in the .itp itself
2. Add the new parameters to the parent force field files

Either is valid, but I suggested #2 because it is easier for people who are 
unfamiliar with topological order requirements to get it all right.  The simple 
idea is "add parameters where all the other parameters are."

Force field parameters have to be defined before they can be used; this is why 
you're not doing "double work."  You have a molecule that requires non-standard 
or non-existent parameters.  You have to tell the force field that there are new 
interaction types available to molecules in the system.  Only then can you 
define molecules that make use of those parameters.  For full details on force 
field hierarchy, see Chapter 5 of the manual.  If you're doing things 
"manually," this chapter is going to be your best friend.

-Justin

> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: Monday, May 25, 2015 7:34 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error using grompp - atomtype not found
>
> On 5/25/15 11:08 AM, Sotirios Dionysios I. Papadatos wrote:
>> Hi,
>>
>> I have made a molecule.itp, which is what I want to run MD calculations on. Meaning I couldn't produce it with pdb2gmx but I rather made a .top with vi editor.
>>
>> When I try to use grompp it says atomtype opls_XXXX not found.
>>
>> I have added all the needed atoms in atomtypes.atp of the ff I want to use. I should also mention that I used an existing atom in atomtypes and then the ones I added. Also I used grep to see if I made any spelling mistakes.
>>
>
> The .atp file is used only by pdb2gmx.  You need to add parameters in
> ffnonbonded.itp for any new atom types; this is what grompp is complaining about.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================